Packages Documentation
DataSHIELD Packages Documentation
Overview
Client Packages
dsBaseClient
Installation command:
# Install dsBaseClient package (client side)
install.packages('dsBaseClient', repos=c(getOption('repos'), 'http://cran.obiba.org'), dependencies=TRUE)
Functions:
- checkClass Checks that an object has the same class in all studies
- colPercent Produces column percentages
- ds.Boole Converts a server-side R object into Boolean indicators
- ds.abs Computes the absolute values of a variable
- ds.asCharacter Converts a server-side R object into a character class
- ds.asDataMatrix Converts a server-side R object into a matrix
- ds.asFactor Converts a server-side numeric vector into a factor
- ds.asFactorSimple Converts a numeric vector into a factor
- ds.asInteger Converts a server-side R object into an integer class
- ds.asList Converts a server-side R object into a list
- ds.asLogical Converts a server-side R object into a logical class
- ds.asMatrix Converts a server-side R object into a matrix
- ds.asNumeric Converts a server-side R object into a numeric class
- ds.assign Assigns an R object to a name in the server-side
- ds.auc Calculates the Area under the curve (AUC)
- ds.boxPlot Draw boxplot
- ds.boxPlotGG Renders boxplot
- ds.boxPlotGG_data_Treatment Take a data frame on the server side an arrange it to pass it to the boxplot function
- ds.boxPlotGG_data_Treatment_numeric Take a vector on the server side an arrange it to pass it to the boxplot function
- ds.boxPlotGG_numeric Draw boxplot with information from a numeric vector
- ds.boxPlotGG_table Draw boxplot with information from a data frame
- ds.bp_standards Calculates Blood pressure z-scores
- ds.c Combines values into a vector or list in the server-side
- ds.cbind Combines R objects by columns in the server-side
- ds.changeRefGroup Changes the reference level of a factor in the server-side
- ds.class Class of the R object in the server-side
- ds.colnames Produces column names of the R object in the server-side
- ds.completeCases Identifies complete cases in server-side R objects
- ds.contourPlot Generates a contour plot
- ds.cor Calculates the correlation of R objects in the server-side
- ds.corTest Tests for correlation between paired samples in the server-side
- ds.cov Calculates the covariance of R objects in the server-side
- ds.dataFrame Generates a data frame object in the server-side
- ds.dataFrameFill Creates missing values columns in the server-side
- ds.dataFrameSort Sorts data frames in the server-side
- ds.dataFrameSubset Sub-sets data frames in the server-side
- ds.densityGrid Generates a density grid in the client-side
- ds.dim Retrieves the dimension of a server-side R object
- ds.dmtC2S Copy a clientside data.frame, matrix or tibble to the serverside
- ds.elspline Basis for a piecewise linear spline with meaningful coefficients
- ds.exists Checks if an object is defined on the server-side
- ds.exp Computes the exponentials in the server-side
- ds.extractQuantiles Secure ranking of a vector across all sources and use of these ranks to estimate global quantiles across all studies
- ds.forestplot Forestplot for SLMA models
- ds.gamlss Generalized Additive Models for Location Scale and Shape
- ds.getWGSR Computes the WHO Growth Reference z-scores of anthropometric data
- ds.glm Fits Generalized Linear Model
- ds.glmPredict Applies predict.glm() to a serverside glm object
- ds.glmSLMA Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA)
- ds.glmSummary Summarize a glm object on the serverside
- ds.glmerSLMA Fits Generalized Linear Mixed-Effect Models via Study-Level Meta-Analysis
- ds.heatmapPlot Generates a Heat Map plot
- ds.hetcor Heterogeneous Correlation Matrix
- ds.histogram Generates a histogram plot
- ds.igb_standards Converts birth measurements to intergrowth z-scores/centiles
- ds.isNA Checks if a server-side vector is empty
- ds.isValid Checks if a server-side object is valid
- ds.kurtosis Calculates the kurtosis of a numeric variable
- ds.length Gets the length of an object in the server-side
- ds.levels Produces levels attributes of a server-side factor
- ds.lexis Represents follow-up in multiple states on multiple time scales
- ds.list Constructs a list of objects in the server-side
- ds.listClientsideFunctions Lists client-side functions
- ds.listDisclosureSettings Lists disclosure settings
- ds.listOpals Lists all Opal objects in the analytic environment
- ds.listServersideFunctions Lists server-side functions
- ds.lmerSLMA Fits Linear Mixed-Effect model via Study-Level Meta-Analysis
- ds.log Computes logarithms in the server-side
- ds.look Performs direct call to a server-side aggregate function
- ds.ls lists all objects on a server-side environment
- ds.lspline Basis for a piecewise linear spline with meaningful coefficients
- ds.make Calculates a new object in the server-side
- ds.matrix Creates a matrix on the server-side
- ds.matrixDet Calculates de determinant of a matrix in the server-side
- ds.matrixDet.report Returns matrix determinant to the client-side
- ds.matrixDiag Calculates matrix diagonals in the server-side
- ds.matrixDimnames Specifies the dimnames of the server-side matrix
- ds.matrixInvert Inverts a server-side square matrix
- ds.matrixMult Calculates tow matrix multiplication in the server-side
- ds.matrixTranspose Transposes a server-side matrix
- ds.mean Computes server-side vector statistical mean
- ds.meanByClass Computes the mean and standard deviation across categories
- ds.meanSdGp Computes the mean and standard deviation across groups defined by one factor
- ds.merge Merges two data frames in the server-side
- ds.message Returns server-side messages to the client-side
- ds.metadata Gets the metadata associated with a variable held on the server
- ds.mice Multivariate Imputation by Chained Equations
- ds.names Return the names of a list object
- ds.ns Generate a Basis Matrix for Natural Cubic Splines
- ds.numNA Gets the number of missing values in a server-side vector
- ds.qlspline Basis for a piecewise linear spline with meaningful coefficients
- ds.quantileMean Computes the quantiles of a server-side variable
- ds.rBinom Generates Binomial distribution in the server-side
- ds.rNorm Generates Normal distribution in the server-side
- ds.rPois Generates Poisson distribution in the server-side
- ds.rUnif Generates Uniform distribution in the server-side
- ds.ranksSecure Secure ranking of a vector across all sources
- ds.rbind Combines R objects by rows in the server-side
- ds.reShape Reshapes server-side grouped data
- ds.recodeLevels Recodes the levels of a server-side factor vector
- ds.recodeValues Recodes server-side variable values
- ds.rep Creates a repetitive sequence in the server-side
- ds.replaceNA Replaces the missing values in a server-side vector
- ds.rm Deletes server-side R objects
- ds.rowColCalc Computes rows and columns sums and means in the server-side
- ds.sample Performs random sampling and permuting of vectors, dataframes and matrices
- ds.scatterPlot Generates non-disclosive scatter plots
- ds.seq Generates a sequence in the server-side
- ds.setDefaultOpals Creates a default set of Opal objects called ‘default.opals’
- ds.setSeed Server-side random number generation
- ds.skewness Calculates the skewness of a server-side numeric variable
- ds.sqrt Computes the square root values of a variable
- ds.subset Generates a valid subset of a table or a vector
- ds.subsetByClass Generates valid subset(s) of a data frame or a factor
- ds.summary Generates the summary of a server-side object
- ds.table Generates 1-, 2-, and 3-dimensional contingency tables with option of assigning to serverside only and producing chi-squared statistics
- ds.table1D Generates 1-dimensional contingency tables
- ds.table2D Generates 2-dimensional contingency tables
- ds.tapply Applies a Function Over a Server-Side Ragged Array
- ds.tapply.assign Applies a Function Over a Ragged Array on the server-side
- ds.testObjExists Checks if an R object exists on the server-side
- ds.unList Flattens Server-Side Lists
- ds.unique Perform ‘unique’ on a variable on the server-side
- ds.var Computes server-side vector variance
- ds.vectorCalc Performs a mathematical operation on two or more vectors
- extract Splits character by ‘$’ and returns the single characters
- getPooledMean Gets a pooled statistical mean
- getPooledVar Gets a pooled variance
- glmChecks Checks if the elements in the glm model have the right characteristics
- isAssigned Checks an object has been generated on the server side
- isDefined Checks if the objects are defined in all studies
- logical2int Turns a logical operator into an integer
- meanByClassHelper0a Computes the mean values of a numeric vector across a factor vector
- meanByClassHelper0b Runs the computation if variables are within a table structure
- meanByClassHelper1 Generates subset tables
- meanByClassHelper2 Generates a table for pooled results
- meanByClassHelper3 Generates results tables for each study separately
- meanByClassHelper4 Gets the subset tables out of the list (i.e. unlist)
- rowPercent Produces row percentages
- subsetHelper Ensures that the requested subset is not larger than the original object
Sources:
dsDangerClient
Installation command:
# Install dsDangerClient package (client side)
install.packages('dsDangerClient', repos=c(getOption('repos'), 'http://cran.obiba.org'), dependencies=TRUE)
Functions:
- ds.DANGERc2sMATDF DANGER FUNCTION copying clientside matrix to serverside
- ds.DANGERdfEXTRACT DANGER function returning data.frame (df) from processing servers to clientside - ** DEPRECATED BY ds.DANGERdmtEXTRACT **
- ds.DANGERdmtEXTRACT DANGER function returning data.frame, Matrix or tibble (DMT) from processing servers to clientside
- ds.DANGERlistcode list the code for a function
- ds.DANGERpassPARSER determines how a given R object or character string is managed by the DataSHIELD parser
- ds.DANGERplot DANGER function
- ds.DANGERprint DANGER function
- ds.DANGERsearch lists all R environments on serverside
- ds.DANGERseedEXTRACT ds.DANGERseedEXTRACT
- ds.DANGERvarsEXTRACT ds.DANGERvarsEXTRACT
Sources:
Server Packages
dsBase
Installation command:
# Install dsBase package (server side)
library(opaladmin)
o<-opal.login(...)
dsadmin.install_package(o, 'dsBase')
Functions:
- BooleDS BooleDS
- absDS Computes the absolute values of the input variable
- asCharacterDS Coerces an R object into class character
- asDataMatrixDS asDataMatrixDS a serverside assign function called by ds.asDataMatrix
- asFactorDS1 Determines the levels of the input variable in each single study
- asFactorDS2 Converts a numeric vector into a factor
- asFactorSimpleDS Converts a numeric vector into a factor
- asIntegerDS Coerces an R object into class integer
- asListDS asListDS a serverside aggregate function called by ds.asList
- asLogicalDS Coerces an R object into class numeric
- asMatrixDS Coerces an R object into a matrix
- asNumericDS Coerces an R object into class numeric
- aucDS aucDS an aggregate function called by ds.auc
- blackBoxDS Secure ranking of “V2BR” (vector to be ranked) across all sources
- blackBoxRanksDS Secure ranking of “V2BR” (vector to be ranked) across all sources
- boxPlotGGDS Create the identity stats and necessary data to draw a plot on the client
- boxPlotGG_data_TreatmentDS Arrange data frame to pass it to the boxplot function
- boxPlotGG_data_Treatment_numericDS Arrange vector to pass it to the boxplot function
- bp_standardsDS Calculates Blood pressure z-scores
- cDS Concatenates objects into a vector or list
- cbindDS cbindDS called by ds.cbind
- changeRefGroupDS Changes a reference level of a factor
- checkNegValueDS Checks if a numeric variable has negative values
- checkPermissivePrivacyControlLevel checkPermissivePrivacyControlLevel
- classDS Returns the class of an object
- colnamesDS Returns the column names of a data frame or matrix
- completeCasesDS completeCasesDS: an assign function called by ds.completeCases
- corDS Computes the sum of each variable and the sum of products for each pair of variables
- corTestDS Tests for correlation between paired samples
- covDS Computes the sum of each variable and the sum of products for each pair of variables
- dataFrameDS dataFrameDS called by ds.dataFrame
- dataFrameFillDS dataFrameFillDS
- dataFrameSortDS Sorting and reordering data frames, vectors or matrices
- dataFrameSubsetDS1 dataFrameSubsetDS1 an aggregate function called by ds.dataFrameSubset
- dataFrameSubsetDS2 dataFrameSubsetDS2 an assign function called by ds.dataFrameSubset
- densityGridDS Generates a density grid with or without a priori defined limits
- dimDS Returns the dimension of a data frame or matrix
- dmtC2SDS Copy a clientside data.frame, matrix or tibble (DMT) to the serverside.
- elsplineDS Basis for a piecewise linear spline with meaningful coefficients
- extract Splits character by ‘$’ and returns the single characters
- extractQuantilesDS1 Secure ranking of “V2BR” (vector to be ranked) across all sources and use of these ranks to estimate global quantiles across all studies
- extractQuantilesDS2 Secure ranking of “V2BR” (vector to be ranked) across all sources and use of these ranks to estimate global quantiles across all studies
- gamlssDS gamlssDS an aggregate function called by ds.galmss
- getWGSRDS Computes the WHO Growth Reference z-scores of anthropometric data
- glmDS1 glmDS1 called by ds.glm
- glmDS2 glmDS2 called by ds.glm
- glmPredictDS.ag predict regression responses from a glm object
- glmPredictDS.as predict regression responses from a glm object
- glmSLMADS.assign Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA)
- glmSLMADS1 Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA)
- glmSLMADS2 Fit a Generalized Linear Model (GLM) with pooling via Study Level Meta-Analysis (SLMA)
- glmSummaryDS.ag summarize a glm object on the serverside
- glmSummaryDS.as summarize a glm object on the serverside
- glmerSLMADS.assign Fitting generalized linear mixed effect models - serverside function
- glmerSLMADS2 Fitting generalized linear mixed effect models - serverside function
- heatmapPlotDS Calculates the coordinates of the centroid of each n nearest neighbours
- hetcorDS Heterogeneous Correlation Matrix
- histogramDS1 returns the minimum and the maximum of the input numeric vector
- histogramDS2 Computes a histogram of the input variable without plotting.
- igb_standardsDS Converts birth measurements to intergrowth z-scores/centiles
- isNaDS Checks if a vector is empty
- isValidDS Checks if an input is valid
- kurtosisDS1 Calculates the kurtosis of a numeric variable
- kurtosisDS2 Calculates the kurtosis of a numeric variable
- lengthDS Returns the length of a vector or list
- levelsDS Returns the levels of a factor vector
- lexisDS1 lexisDS1
- lexisDS2 lexisDS2
- lexisDS3 @title lexisDS3
- listDS Coerce objects into a list
- listDisclosureSettingsDS listDisclosureSettingsDS
- lmerSLMADS.assign Fitting linear mixed effect models - serverside function
- lmerSLMADS2 Fitting linear mixed effect models - serverside function
- lsDS lists all objects on a serverside environment
- lsplineDS Basis for a piecewise linear spline with meaningful coefficients
- matrixDS matrixDS assign function called by ds.matrix
- matrixDetDS1 matrixDetDS aggregate function called by ds.matrixDet.report
- matrixDetDS2 matrixDetDS assign function called by ds.matrixDet
- matrixDiagDS matrixDiagDS assign function called by ds.matrixDiag
- matrixDimnamesDS matrixDimnamesDS assign function called by ds.matrixDimnames
- matrixInvertDS matrixInvertDS serverside assign function called by ds.matrixInvert
- matrixMultDS matrixMultDS serverside assign function called by ds.matrixMult
- matrixTransposeDS matrixTransposeDS serverside assign function called by ds.matrixTranspose
- meanDS Computes statistical mean of a vectores
- meanSdGpDS MeanSdGpDS
- mergeDS mergeDS (assign function) called by ds.merge
- messageDS messageDS
- metadataDS Returns the metadata, if any, about the specified variable
- miceDS Aggregate function called by ds.mice
- minMaxRandDS Secure ranking of “V2BR” (vector to be ranked) across all sources
- namesDS Return the names of a list object
- nsDS Generate a Basis Matrix for Natural Cubic Splines
- numNaDS Counts the number of missing values
- qlsplineDS Basis for a piecewise linear spline with meaningful coefficients
- quantileMeanDS Generates quantiles and mean information without maximum and minimum
- rBinomDS rBinomDS serverside assign function
- rNormDS rNormDS serverside assign function
- rPoisDS rPoisDS serverside assign function
- rUnifDS rUnifDS serverside assign function
- rangeDS returns the minimum and maximum of a numeric vector
- ranksSecureDS1 Secure ranking of “V2BR” (vector to be ranked) across all sources
- ranksSecureDS2 Secure ranking of “V2BR” (vector to be ranked) across all sources
- ranksSecureDS3 Secure ranking of “V2BR” (vector to be ranked) across all sources
- ranksSecureDS4 Secure ranking of “V2BR” (vector to be ranked) across all sources
- ranksSecureDS5 Secure ranking of “V2BR” (vector to be ranked) across all sources
- rbindDS rbindDS called by ds.rbind
- reShapeDS reShapeDS (assign function) called by ds.reShape
- recodeLevelsDS Recodes the levels of a categorical variables
- recodeValuesDS recodeValuesDS an assign function called by ds.recodeValues
- repDS repDS called by ds.rep
- replaceNaDS Replaces the missing values in a vector
- rmDS rmDS an aggregate function called by ds.rm
- rowColCalcDS Computes sums and means of rows or columns of numeric arrays
- sampleDS random sampling and permuting of vectors, dataframes and matrices
- scatterPlotDS Calculates the coordinates of the data to be plot
- seqDS seqDS a serverside assign function called by ds.seq
- setFilterDS Sets the privacy level
- setSeedDS setSeedDs called by ds.setSeed, ds.rNorm, ds.rUnif, ds.rPois and ds.rBinom
- skewnessDS1 Calculates the skewness of a numeric variable
- skewnessDS2 Calculates the skewness of a numeric variable
- sqrtDS Computes the square root values of the input variable
- subsetByClassDS Breaks down a dataframe or a factor into its sub-classes
- subsetByClassHelper1 generates subsets vectors from a factor vector
- subsetByClassHelper2 generates subset tables from a data frame
- subsetByClassHelper3 generates subset tables from a data frame
- subsetDS Generates a valid subset of a table or a vector
- table1DDS Creates 1-dimensional contingency tables
- table2DDS table2DDS (aggregate function) called by ds.table2D
- tableDS tableDS is the first of two serverside aggregate functions called by ds.table
- tableDS.assign tableDS.assign is the serverside assign function called by ds.table
- tableDS2 tableDS is the second of two serverside aggregate functions called by ds.table
- tapplyDS tapplyDS called by ds.tapply
- tapplyDS.assign tapplyDS.assign called by ds.tapply.assign
- testObjExistsDS testObjExistsDS
- unListDS unListDS a serverside assign function called by ds.unList
- uniqueDS Applies the ‘unique’ method to a server-side variable.
- varDS Computes the variance of vector
- vectorDS Creates a vector on the server-side.
Sources:
dsDanger
Installation command:
# Install dsDanger package (server side)
library(opaladmin)
o<-opal.login(...)
dsadmin.install_package(o, 'dsDanger')
Functions:
- DANGERc2sMATDFDS DANGER FUNCTION copying clientside matrix to serverside
- DANGERdfEXTRACTDS DANGER function returning data.frame (df) from processing servers to clientside - ** DEPRECATED DANGERdmtEXTRACTDS **
- DANGERdmtEXTRACTDS DANGER function returning data.frame, Matrix or tibble (DMT) from processing servers to clientside
- DANGERlistcodeDS lists the code for a function
- DANGERpassPARSERDS determines how a given R object or character string is managed by the DataSHIELD parser
- DANGERplotDS DANGERplotDS
- DANGERprintDS DANGERprintDS
- DANGERsearchDS lists all environments on serverside
- DANGERseedEXTRACTDS DANGERseedEXTRACT
- DANGERvarsEXTRACTDS DANGERvarsEXTRACT
Sources: